chore: python project migration to uv

[neo-jesse]

Migrate Python dependency management from Pipenv to UV

Summary

Migrates api and shared-data projects from pipenv to uv for faster dependency resolution and installation. All other projects continue using pipenv.

Key Changes for Api and shared-data

• Migrated api and shared-data from Pipfile to pyproject.toml with uv.lock
• Created scripts/python-uv.mk for UV projects; scripts/python.mk remains for pipenv projects
• Updated GitHub Actions setup action to detect project type (UV vs pipenv) and install dependencies accordingly
• Fixed dependencies: added opentrons-hardware[FLEX] to api dev deps, numpy to shared-data main deps
• Fixed mypy errors (redundant casts, unused ignores, untyped decorators)
• Migrated JSON schema validation from jsonschema.RefResolver to referencing library
• Refactored GitHub Actions Python setup into modular actions (install-uv, cache-uv, setup)
• Fixed Windows PATH issues for uv in Make commands
• Added install-dev-deps: 'true' to workflows that run lint/test for UV projects

Changes for Pipenv Projects

• Updated all pipenv Makefiles to use pipenv sync --dev to ensure dev dependencies are installed
• Fixed workflows to properly install dev dependencies for lint/test jobs

Benefits

• Faster dependency resolution and installation for api and shared-data
• Standardized pyproject.toml configuration for migrated projects
• Improved CI reliability with proper caching and dev dependency handling
• Gradual migration path - other projects can be migrated incrementally

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 25.97%. Comparing base (50eea15) to head (28d0881).

Additional details and impacted files

@@                  Coverage Diff                  @@
##           bump-to-scarthgap   #20135      +/-   ##
=====================================================
+ Coverage              25.96%   25.97%   +0.01%     
=====================================================
  Files                   3641     3640       -1     
  Lines                 303277   303167     -110     
  Branches               42379    42588     +209     
=====================================================
+ Hits                   78735    78737       +2     
+ Misses                224519   224407     -112     
  Partials                  23       23              

Flag	Coverage Δ
app	2.09% <ø> (-0.01%)	⬇️
protocol-designer	19.38% <ø> (ø)
step-generation	5.62% <ø> (ø)
update-server	63.34% <ø> (-0.29%)	⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.
see 12 files with indirect coverage changes

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[sfoster1]

let's try and do all we can to avoid changes that aren't necessary for the uv cutover. that's stuff like

• Altering the pipenv_opts definition requiring changes to all the makefiles to push --dev up
• Whatever is causing the typechecking to change and requiring some extra casts
• Whatever made us reformat ot3controller.py

There's also some other little stuff:

• is there ever a time we would not want to install dev dependencies? can we just remove that argument to the action, or invert it to no-install-dev-deps and specify it more rarely?
• let's rely on python depspecs for the linux only dependencies
• some code duplication around path specification i think we can pull
• let's just double check that the versions of all the dependencies, including dev dependencies, are the same in the new uv and the old pipenv dependency specs. that will let us change fewer things at one time

[sfoster1]

can we probe for the existence of a uv.lock file instead, or even cut over the makefile

[neo-jesse]

More than just the 2 projects we are looking at have uv.lock, it's not a good indicator.

[sfoster1]

Very much getting there! A couple little nits to pick; the only big things left are some github actions stuff, the thing with the mypy configuration in api, and a weirdness with the dependencies in api.